STFT objects are created by the stft function. These methods print some useful summary statistics about them, and produce plots.mode determines the type of plot. "decibel" and "modulus" work with the raw values, while "pvalue" conducts some degree of normalisation in each time window and so is perhaps more useful for data showing a large variation in sd across different points in time. If the null.calc was set in the original stft argument, that is used - otherwise, an Exponential distribution is fit to each window, and the pvalues computed from that.
By default, the function uses some empirical quantile based colour thresholds designed to give somewhat reasonable and informative plots. This can be overridden, however, by setting different zlim.raw or zlim.quantile results. This can be useful for comparing two different datasets.
Reassigned stft plots are constructed, by default, when they are available, and when the original was not a "mv" stft. Unlike the heatmap used in the usual stft plot, a 2d scatterplot is used instead. This means that if there are few data points, it can be advantageous to set a higher cex value for larger points and better display.
With Accelerometer data, often the frequencies of interest are concentrated at the lower frequencies. Topthresh crops the frequency display to show only those frequencies. A summary plot is show on the top, to compensate. Choosing a grid of frequencies, this plot draws one line to represent the energies present in the signal at that particular frequency, and higher. Black lines are drawn for frequencies less than 2/3 the topthresh, red lines for 2/3 - 1 times topthresh, and blue lines for frequencies higher than topthresh. Alternative, set log = "y" to put frequencies on a log scale.